Showing : GenomicAlignments • reset
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How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 9 months ago by 16k • written 9 months ago by • 0
4
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2
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1.5k
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GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
9 months ago pineiroalejandro ▴ 10
1
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2
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1.4k
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Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
12 months ago SofieK • 0
4
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5
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1.6k
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Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
3.1 years ago • updated 3.0 years ago Robert Castelo ★ 3.4k
1
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0
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987
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Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
3.4 years ago chen_ying ▴ 10
3
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4
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1.7k
views
mapToAlignments_issue
GenomicAlignments
updated 3.5 years ago by 16k • written 3.6 years ago by • 0
0
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1
reply
1.9k
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Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 3.7 years ago by • 0 • written 3.7 years ago by • 0
0
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9
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2.7k
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Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
3.9 years ago • updated 3.7 years ago Jiping Wang ▴ 90
1
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0
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1.7k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.9 years ago L ▴ 50
0
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1
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3.8k
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Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 3.6 years ago by • 0 • written 4.1 years ago by • 0
0
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0
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1.0k
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
4.8 years ago Malcolm Perry ▴ 40
0
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1
reply
2.8k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
4.9 years ago Matthias Munz ▴ 20
0
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2
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1.4k
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Visualising read alignments in
GenomicAlignments Rsamtools
written 4.9 years ago by • 0
4
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4
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5.9k
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 5.0 years ago by ▴ 20
0
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3
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1.4k
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
5.2 years ago Marco Blanchette ▴ 30
0
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0
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1.4k
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
5.6 years ago dequattro.concetta ▴ 10
0
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0
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2.1k
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
1
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2
replies
1.4k
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Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 10
4
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4
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2.6k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.9 years ago Konstantinos Yeles ▴ 90
2
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2
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2.4k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 6.0 years ago by 16k • written 6.0 years ago by • 0
0
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8
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2.8k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 90
0
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2
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1.3k
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 40
4
votes
6
replies
2.8k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 6.3 years ago by ▴ 740 • written 6.3 years ago by ▴ 40
1
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2
replies
2.1k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 6.4 years ago by ★ 11k • written 8.9 years ago by ▴ 10
0
votes
4
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1.5k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 90
1
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9
replies
2.3k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
6.7 years ago Janet Young ▴ 740
1
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8
replies
4.2k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 6.7 years ago by 16k • written 6.7 years ago by ▴ 90
4
votes
4
replies
1.9k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 6.7 years ago by 25k • written 6.7 years ago by ★ 1.6k
0
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9
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2.2k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
3
votes
3
replies
1.6k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 100
3
votes
2
replies
1.6k
views
Error in summarizeOverlaps
GenomicAlignments
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
2
votes
1
reply
1.6k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 6.9 years ago by 25k • written 6.9 years ago by 68k
0
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2
replies
1.4k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
6.9 years ago Christian Mertes • 0
2
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3
replies
1.8k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 7.0 years ago by ★ 6.6k • written 7.0 years ago by ▴ 80
1
vote
3
replies
1.7k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ★ 3.4k
0
votes
1
reply
1.7k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by • 0
0
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2
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1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.4 years ago A ▴ 60
0
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2
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1.8k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 7.5 years ago by 16k • written 7.5 years ago by • 0
1
vote
1
reply
2.4k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 30
0
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1
reply
1.2k
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
7.5 years ago martin.busch • 0
2
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2
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1.7k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ★ 7.9k
0
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0
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1.6k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
1
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4
replies
2.0k
views
error displaying bam files
genomicalignments
8.3 years ago • updated 8.2 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
3.4k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
8.3 years ago Robert Castelo ★ 3.4k
2
votes
4
replies
2.4k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ★ 3.4k
2
votes
9
replies
3.0k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 20
0
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0
replies
1.5k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
8.4 years ago igor ▴ 50
5
votes
4
replies
3.8k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by ★ 3.4k
2
votes
5
replies
2.4k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
2
votes
1
reply
1.7k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 90
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
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